Differential structuring of human populations for homologous X and Y microsatellite loci.

The global pattern of variation at the homologous microsatellite loci DYS413 (Yq11) and DXS8174 and DXS8175 (Xp22) was analyzed by examination of 30 world populations from four continents, accounting for more than 1,100 chromosomes per locus. The data showed discordant patterns of among- and within-population gene diversity for the Y-linked and the X-linked microsatellites. For the Y-linked polymorphism, all groups of populations displayed high FST values (the correlation between random haplotypes within subpopulations, relative to haplotypes of the total population) and showed a general trend for the haplotypes to cluster in a population-specific way. This was especially true for sub-Saharan African populations. The data also indicated that a large fraction of the variation among populations was due to the accumulation of new variants associated with the radiation process. Europeans exhibited the highest level of within-population haplotype diversity, whereas sub-Saharan Africans showed the lowest. In contrast, data for the two X-linked polymorphisms were concordant in showing lower FST values, as compared with those for DYS413, but higher within-population variances, for African versus non-African populations. Whereas the results for the X-linked loci agreed with a model of greater antiquity for the African populations, those for DYS413 showed a confounding pattern that is apparently at odds with such a model. Possible factors involved in this differential structuring for homologous X and Y microsatellite polymorphisms are discussed.     

Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby

The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been isolated on several islands off the Western Australian and South Australian coastlines for between 10 000 and 13 000 years. Here, we combine analyses of autosomal, Y-linked and X-linked microsatellite loci to investigate genetic variation in populations of this species on two islands (Kangaroo Island, South Australia and Garden Island, Western Australia). All measures of diversity were higher for the larger Kangaroo Island population, in which genetic variation was lowest at Y-linked markers and highest at autosomal markers (θ=3.291, 1.208 and 0.627 for autosomal, X-linked and Y-linked data, respectively). Greater relatedness among females than males provides evidence for male-biased dispersal in this population, while sex-linked markers identified genetic lineages not apparent from autosomal data alone. Overall genetic diversity in the Garden Island population was low, especially on the Y chromosome where most males shared a common haplotype, and we observed high levels of inbreeding and relatedness among individuals. Our findings highlight the utility of this approach for management actions, such as the selection of animals for translocation or captive breeding, and the ecological insights that may be gained by combining analyses of microsatellite markers on sex chromosomes with those derived from autosomes.     

Indirect evidence from DNA sequence diversity for genetic degeneration of the Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs

The action of natural selection is expected to reduce the effective population size of a nonrecombining chromosome, and this is thought to be the chief factor leading to genetic degeneration of Y-chromosomes, which cease recombining during their evolution from ordinary chromosomes. Low effective population size of Y chromosomes can be tested by studying DNA sequence diversity of Y-linked genes. In the dioecious plant, Silene latifolia, which has sex chromosomes, one comparison (SlX1 vs. SlY1) indeed finds lower Y diversity compared with the homologous X-linked gene, and one Y-linked gene with no X-linked homologue has lower species-wide diversity than a homologous autosomal copy (SlAp3Y vs. SlAp3A). To test whether this is a general pattern for Y-linked genes, we studied two further recently described X and Y homologous gene pairs in samples from several populations of S. latifolia and S. dioica. Diversity is reduced for both Y-linked genes, compared with their X-linked homologues. Our new data are analysed to show that the low Y effective size cannot be explained by different levels of gene flow for the X vs. the Y chromosomes, either between populations or between these closely related species. Thus, all four Y-linked genes that have now been studied in these plants (the two studied here, and two previously studied genes, have low diversity). This supports other evidence for an ongoing degeneration process in these species.     

Characterization of a Small Family (CAIII) of Microsatellite-Containing Sequences with X-Y Homology

Four X-linked loci showing homology with a previously described Y-linked polymorphic locus (DYS413) were identified and characterized. By fluorescent in situ hybridization (FISH), somatic cell hybrids, and YAC screening, the X-linked members of this small family of sequences (CAIII) all map in Xp22, while the Y members map in Yq11. These loci contribute to the overall similarity of the two genomic regions. All of the CAIII loci contain an internal microsatellite of the (CA)_n type. The microsatellites display extensive length polymorphism in two of the X-linked members as well as in the Y members. In addition, common sequence variants are found in the portions flanking the microsatellites in two of the X-linked members. Our results indicate that, during the evolution of this family, length variation on the Y chromosome was accumulated at a rate not slower than that on the X chromosome. Finally, these sequences represent a model system with which to analyze human populations for similar X- and Y-linked polymorphisms. Received: 29 July 1996 / Accepted: 15 January 1997     

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.     

Genome-wide distribution of linkage disequilibrium in the population of Palau and its implications for gene flow in Remote Oceania

Linkage disequilibrium (LD) between alleles on the same human chromosome results from various evolutionary processes and is thus telling about the history of populations. Recently, LD has garnered substantial interest for its value to map and fine-map disease genes. We examine the distribution of LD between short tandem repeat alleles on autosomes and sex chromosomes in the Remote Oceanic population of Palau to evaluate whether the data are consistent with a recent hypothesis about the origins of genetic variation in Palau, specifically that the population experienced extensive male-biased gene flow following initial settlement. Consistent with evolutionary theory based on effective population size, LD between X-linked alleles is stochastically greater than LD between autosomal alleles, however, small but detectable LD occurs for autosomal markers separated by substantial distances. By contrast, while Y-linked alleles experience only one-third the effective population size of X-linked alleles, their mean value for pairwise LD is only slightly larger than X-linked alleles. For a small population known to experience at least two extreme bottlenecks, 56 six-locus Y haplotypes exhibit remarkable diversity (0.96), comparable to Y diversity of Europeans, however, autosomal and X-linked markers display significantly less diversity, as measured by heterozygosity (4.1% less). Palauan Y haplotypes also fall into distinct clusters, again unlike that of Europe. We argue these data are consistent with waves of male-biased gene flow.     

中国地方黄牛的Y染色体遗传多样性及其进化起源

中国黄牛的进化起源与遗传多样性一直是国内外动物遗传学家感兴趣的课题之一.本文主要从Y染色体的形态多样性和Y染色体特异性微卫星标记遗传多态性两个方面对中国地方黄牛的遗传多样性和进化起源进行了综述.中国地方黄牛Y染色体具有中着丝粒、亚中着丝粒和近端着丝粒3种类型,这说明中国地方黄牛起源于普通牛和瘤牛.利用Y染色体特异性微卫星标记对中国地方黄牛Y染色体单倍型分布特征及Y染色体基因流模式的分析表明,北方种群中普通牛单倍型频率最高,瘤牛单倍型在南方种群中占优势;在中国不同地域,瘤牛Y染色体单倍型频率呈现自南而北、自东而西逐渐降低的趋势,这再次证实了中国黄牛主要来源于普通牛和瘤牛,这可能是这两类牛群在长期的历史进化过程中,分别从东南方向和西北方向进入我国,并在中原地区汇合的结果.本文为中国地方黄牛品种资源保护和杂交育种工作提供了参考依据.     

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes'' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.     

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (approximately 14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (approximately 8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.     

沼泽型水牛Y染色体微卫星标记的筛选与多态性检测

为了研究水牛Y染色体的遗传多样性, 文章以滇东南水牛3个地方群体- 红河(HH)、西双版纳(BN)和普洱(PR)共31头公牛为研究对象, 选取14个家牛Y染色体特异性微卫星标记, 以检测这些标记在水牛Y染色体遗传多样性研究中的可行性。结果表明, 3个标记(INRA008、UMN0103和UMN0504)只有1个等位基因, 表现为单态; 3个标记(UMN1113、UMN0304和BC1.2)均为3个等位基因, 但呈单态; 3个标记(UMN0920、UMN0307和UMN3008)呈现无规律的梯状条带, 所以这9个标记都不适用于水牛的Y染色体遗传多样性研究; 只有5个标记(INRA124、INRA189、BM861、PBR1F1和UMN2001)具有多态性, 表明适用于水牛的Y染色体遗传多样性研究。这5个多态性Y染色体特异微卫星标记在滇东南水牛群体中的平均等位基因数(NA)为2.8000, 平均期望杂合度(He)为0.3998, 基因多样性(GD)为0.4144, 多态信息含量(PIC)为0.3245, Shannon信息熵(SI)为0.5849, 表明滇东南水牛群体的Y染色体具有中等遗传多态性。     

Molecular characterization and population study of an X chromosome homolog of the Y-linked microsatellite DYS391

A novel microsatellite homologous to DYS391, a (GATA)(n) short tandem repeat on the human Y chromosome, was identified and characterized in the present work. Employing somatic cell hybrid and deletion panels in a PCR-based approach, we found out that the new microsatellite is located in Xp21.2-22.3, while its Y counterpart mapped to Yq11.21. This X-linked locus (provisionally called DXYS391) and its Y homolog constitute one more example of similarity outside the pseudoautosomal regions between the two human sex chromosomes. Sequencing data showed high levels of homology in the flanking regions of DXYS391 and DYS391 that differ primarily by the presence of a (GACA)(3) motif in the Y locus. Both loci were detected in chimpanzee DNA, suggesting that a putative transposition from the X to the Y occurred before the human/chimpanzee split. The allele frequencies of DYS391 and DXYS391 were investigated, respectively, in 271 Y and 337 X chromosomes from distinct human populations worldwide. DYS391 consistently displayed greater among-population component of the variance of the allele frequencies than DXYS391, as expected due to the three-times lower effective population size of Y chromosomes relative to the X. The intra-population diversity of DYS391, measured by Nei's locus diversity as well as by allele size variance, was lowest in Amerindians, while very low diversity of DXYS391 was seen in Africans. Since our African data are based on a small sample, further studies will be necessary to evaluate better this observation.     

Development of Y chromosome intraspecific polymorphic markers in the Felidae

Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.     

Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes

Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ～10 million years ago and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of an S. latifolia inbred line to detect sex-linked SNPs and identified more than 1,700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes.     

African and Levantine origins of Pakistani YAP+ Y chromosomes.

We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.     

Y chromosome haplotype analysis in Portuguese cattle breeds using SNPs and STRs

DNA samples from 307 males of 13 Portuguese native cattle breeds, 57 males of the 3 major exotic breeds in Portugal (Charolais, Friesian, and Limousin), and 5 Brahman (Bos indicus) were tested for 5 single nucleotide polymorphisms, 1 "indel," and 7 microsatellites specific to the Y chromosome. The 13 Y-haplotypes defined included 3 previously described patrilines (Y1, Y2, and Y3) and 10 new haplotypes within Bos taurus. Native cattle contained most of the diversity with 7 haplotypes (H2Y1, H3Y1, H5Y1, H7Y2, H8Y2, H10Y2, and H12Y2) found only in these breeds. H6Y2 and H11Y2 occurred in high frequency across breeds including the exotics. Introgression of Friesian cattle into Ramo Grande was inferred through their sharing of haplotype H4Y1. Among the native breeds, Mertolenga had the highest haplotype diversity (0.68 +/- 0.07), Brava de Lide was the least differentiated. The analyses of molecular variance showed significant (P < 0.0001) differences between breeds with more than 64% of the total genetic variation found among breeds within groups and 33-35% within breeds. The detection of INRA189-104 allele in 8 native breeds suggested influence of African cattle in breeds of the Iberian Peninsula. The presence in Portuguese breeds of Y1 patrilines, also found in aurochs, could represent more ancient local haplotypes.     

The Sex-Ratio Trait in Drosophila Simulans: Genetic Analysis of Distortion and Suppression

The sex-ratio trait described in several Drosophila species is a type of naturally occurring X-linked meiotic drive that causes males bearing a sex-ratio X chromosome to produce progenies with a large excess of females. We have previously reported the occurrence of sex-ratio X chromosomes in Drosophila simulans. In this species, because of the co-occurrence of drive suppressors, the natural populations and the derived laboratory strains show an equal sex-ratio even when sex-ratio X chromosomes are present at a high frequency. The presence of sex-ratio X chromosomes is established via crosses with a standard strain that is devoid of drive suppressors. In this article, we show first that the sex-ratio trait in D. simulans results from the action of several X-linked loci. Second we describe drive suppressors on each major autosome as well as on the Y chromosome. The Y-linked factors suppress the drive partially whereas the autosomal suppression can be complete.     

The Y chromosomes of Drosophila simulans are highly polymorphic for their ability to suppress sex-ratio drive

The sex-ratio trait, known in several species of Drosophila including D. simulans, results from meiotic drive of the X chromosome against the Y. Males that carry a sex-ratio X chromosome produce strongly female-biased progeny. In D. simulans, drive suppressors have evolved on the Y chromosome and on the autosomes. Both the frequency of sex-ratio X and the strength of the total drive suppression (Y-linked and autosomal) vary widely among geographic populations of this worldwide species. We have investigated the pattern of Y-linked drive suppression in six natural populations representative of this variability. Y-linked suppressors were found to be a regular component of the suppression, with large differences between populations in the mean level of suppression. These variations did not correspond to differences in frequency of discrete types of Y chromosomes, but to a more or less wide continuum of phenotypes, from nonsuppressor to partial or total suppressor. We concluded that a large diversity of Y-linked suppressor alleles exists in D. simulans and that some populations are highly polymorphic. Our results support the hypothesis that a Y-chromosome polymorphism can be easily maintained by a balance between meiotic drive and the cost of drive suppression.     

Dmrt1 polymorphism and sex‐chromosome differentiation in Rana temporaria

Sex‐determination mechanisms vary both within and among populations of common frogs, opening opportunities to investigate the molecular pathways and ultimate causes shaping their evolution. We investigated the association between sex‐chromosome differentiation (as assayed from microsatellites) and polymorphism at the candidate sex‐determining gene Dmrt1 in two Alpine populations. Both populations harboured a diversity of X‐linked and Y‐linked Dmrt1 haplotypes. Some males had fixed male‐specific alleles at all markers (“differentiated” Y chromosomes), others only at Dmrt1 (“proto‐” Y chromosomes), while still others were genetically indistinguishable from females (undifferentiated X chromosomes). Besides these XX males, we also found rare XY females. The several Dmrt1 Y haplotypes differed in the probability of association with a differentiated Y chromosome, which we interpret as a result of differences in the masculinizing effects of alleles at the sex‐determining locus. From our results, the polymorphism in sex‐chromosome differentiation and its association with Dmrt1, previously inferred from Swedish populations, are not just idiosyncratic features of peripheral populations, but also characterize highly diverged populations in the central range. This implies that an apparently unstable pattern has been maintained over long evolutionary times.     

Sex‐chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea)

Occasional XY recombination is a proposed explanation for the sex‐chromosome homomorphy in European tree frogs. Numerous laboratory crosses, however, failed to detect any event of male recombination, and a detailed survey of NW‐European Hyla arborea populations identified male‐specific alleles at sex‐linked loci, pointing to the absence of XY recombination in their recent history. Here, we address this paradox in a phylogeographic framework by genotyping sex‐linked microsatellite markers in populations and sibships from the entire species range. Contrasting with postglacial populations of NW Europe, which display complete absence of XY recombination and strong sex‐chromosome differentiation, refugial populations of the southern Balkans and Adriatic coast show limited XY recombination and large overlaps in allele frequencies. Geographically and historically intermediate populations of the Pannonian Basin show intermediate patterns of XY differentiation. Even in populations where X and Y occasionally recombine, the genetic diversity of Y haplotypes is reduced below the levels expected from the fourfold drop in copy numbers. This study is the first in which X and Y haplotypes could be phased over the distribution range in a species with homomorphic sex chromosomes; it shows that XY‐recombination patterns may differ strikingly between conspecific populations, and that recombination arrest may evolve rapidly (<5000 generations).